ddRAD sequencing-based genotyping for population structure analysis in cultivated tomato provides new insights into the genomic diversity of Mediterranean ‘da serbo’ type long shelf-life germplasm

Abstract

Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections. Using this methodology, we investigated the genomic diversity of a panel of 288 diverse tomato (Solanum lycopersicum L.) accessions enriched in 'da serbo' (called 'de penjar' in Spain) long shelf life (LSL) materials (152 accessions) mostly originating from Italy and Spain. The rest of the materials originate from different countries and include landraces for fresh consumption, elite cultivars, heirlooms, and breeding lines. Apart from their LSL trait, 'da serbo' landraces are of remarkable interest for their resilience. We identified 32,799 high-quality SNPs, which were used for model ancestry population structure and non-parametric hierarchical clustering. Six genetic subgroups were revealed, clearly separating most 'da serbo' landraces, but also the Spanish germplasm, suggesting a subdivision of the population based on type and geographical provenance. Linkage disequilibrium (LD) in the collection decayed very rapidly within <5 kb. We then investigated SNPs showing contrasted minor frequency allele (MAF) in 'da serbo' materials, resulting in the identification of high frequencies in this germplasm of several mutations in genes related to stress tolerance and fruit maturation such as CTR1 and JAR1. Finally, a mini-core collection of 58 accessions encompassing most of the diversity was selected for further exploitation of key traits. Our findings suggest the presence of a genetic footprint of the 'da serbo' germplasm selected in the Mediterranean basin. Moreover, we provide novel insights on LSL 'da serbo' germplasm as a promising source of alleles for tolerance to stresses.

Variation for Composition and Quality in a Collection of the Resilient Mediterranean ‘de penjar’ Long Shelf-Life Tomato Under High and Low N Fertilization Levels

“…Considerable phenotypic variation was observed in our collection for most of the traits evaluated, which is in agreement with the large genetic diversity described for 'de penjar' tomato in other works (Casals et al, 2012;Cebolla-Cornejo et al, 2013;Esposito et al, 2020). Genotyping data of our collection would have been relevant to confirm at the genetic level the high diversity we have found.…”

Breeding for Nutritional and Organoleptic Quality in Vegetable Crops: The Case of Tomato and Cauliflower

“…In the framework of those projects, traditional tomato germoplasm resources characterized by high resilience (e.g., Spanish and Italian 'da serbo' Landraces) as well as accessions of underexploited genetic reservoirs and derived populations (the wild species Solanum pimpinellifolium and Solanum cheesmaniae and the weedy S. lycopersicum var. cerasiforme) have been deeply genotyped for further use in organic breeding programs [22][23][24][25][26].…”

Accelerating Tomato Breeding by Exploiting Genomic Selection Approaches

“…However, the lack of enough DNA markers that detect polymorphism within the cultivated species remains a major issue in tomato crop [10]. Thus, most recently significant efforts were attempted to exploit intraspecific high-resolution genetic markers such as Single Nucleotide Polimorphisms (SNPs) and Insertion and Deletion (InDels to detect polymorphism among closely related individuals [11,12].…”